I am looking to design my own customisation on home page and i want to customise it with my own looks. I have a css file and i would also like to add some jquery functionality to it. So how can i add these files to my home page. eg without magento I would have done it in this way

You can also add Zifius's example into the particular cms page Layout Update XML textfield(Design Tab under CMS/Pages/pagename). Might make it easier to change when there is a strict deployment process in place and you don't want to bother with syncing your repos and deploying the changes.